Welcome to the Xtra Library for
Thermo Scientific Amira, Avizo and PerGeos Software

Below you will find a collection of add-ons (recipes, scripts, demos,…) that will help you improve your day-to-day use of Amira-Avizo and PerGeos Software and make you gain both time and efficiency.
Use the Search field to look for specific keywords related to your domain of interest. The different filters also help you target specific resources.

View Manager

View Manager

Tcl

This module allows storing and retrieving camera settings for viewer windows to be able to switch easily between different view presets.

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Load a Numpy array into PerGeos/Amira-Avizo using the Python API

Load a Numpy array into PerGeos/Amira-Avizo using the Python API

Python (pyscro)

This script simply reads and loads numpy arrays in a user specified directory into PerGeos/Amira-Avizo as an image.

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BSE SEM denoiser

BSE SEM denoiser

Deep learning model

U-Net model for denoising back-scattered SEM images.

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Random Forests for Multiclass Segmentation using Python API in PerGeos

Random Forests for Multiclass Segmentation using Python API in PerGeos

Python (pyscro), Project (hx, pgo), Data

Simple demonstration of feature computation where the feature vector contains intensity and 2D eigenvalues (X & Y). This example uses random forests implementation from the sklearn package.

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PerGeos TCL script for processing all files in a folder with a recipe

PerGeos TCL script for processing all files in a folder with a recipe

Tcl

Process all files in a folder by applying the same recipe to all of them individually.

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Eagleford Shale FIB-SEM Segmentation

Eagleford Shale FIB-SEM Segmentation

Recipe (hxrecipe)

This recipe guided workflow will result in a 5-phase segmentation applicable to the included dataset and most typical FIB-SEM data. Input Data, the Recipe, Output data are included here.

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Berea Pore Size Distribution Tutorial

Berea Pore Size Distribution Tutorial

Recipe (hxrecipe), Project (hx, pgo), Demo, Data

Create a semi-automatic workflow for Pore Size Distribution on Berea sandstone

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Getting Started with Deep Learning Training

Getting Started with Deep Learning Training

Deep learning model, Data

Model and companion project for the Deep Learning tutorial.

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